Foy described working on the Netflix series as the "the most extraordinary two-and-a-half years of my life" while she dedicated the award to "the next cast, the next generation" as well as her on-screen husband Matt Smith, who looked adorably delighted with the mention.
Television's biggest night could end up with its smallest audience ever.
The Marvelous Mrs. Maisel creator Amy Sherman-Palladino led the individual awards with four, followed, with three each, by Late Late Show host and producer James Corden and Amy Entelis, executive producer of Anthony Bourdain: Parts Unknown and United Shades Of America With W. Kamau Bell.
"Maisel", a freshman sitcom about an unhappy 1950s homemaker liberated by stand-up comedy, earned best actress honors for star Rachel Brosnahan.
Hurricane Florence makes landfall in N.Carolina
By late afternoon, Beaufort County Manager Brian Alligood hoped the worst was over. "We have started to see the water recede". The center of Florence is forecast to move further inland across southeastern North Carolina and eastern SC through Saturday.
And last year's "SNL" champs Alec Baldwin and Kate McKinnon were felled by Henry Winkler ("Barry") and Alex Borstein ("The Marvelous Mrs. Maisel").
"This wasn't supposed to happen", said a startled Foy.
Che said it was great to celebrate with all of Hollywood, or at least, the people "who haven't gotten caught yet", and Jost later said that Netflix's huge number of nominations was the worst thing a network executive could hear, "Except maybe, 'Sir, Ronan Farrow is on Line 1'".
John Oliver, in picking up the trophy for best variety talk show award for "Last Week Tonight", thanked Weiss' girlfriend for giving the right answer or, he joked, the whole ceremony could have gone south.
Other big winners included FX's The Assassination of Gianni Versace, which won Emmys for best limited series and an acting prize for Darren Criss, who earned rave reviews for his dark turn as the designer's killer Andrew Cunanan.